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Hard Drive Install Help

I just installed a Quantum ata 100 HD. My MB supports ata66 and when I boot up it shows the HD as secondary master. When I go into my computer it doesn't show up. I have an ata cable and the jumper on the HD is set correctly. Any idea what is wrong? Thanks.

My secondary ide socket is bad on my MB. I just switched it to the primary and now it shows up. I do have another question though. I am getting this for my new drive-Drive D is using MS-DOS compatibility mode file system. What do I have to do to get rid of this message? Thanks for the help.

Now this message- Drive D is using MS-DOS compatibility mode file system is gone, and my drive is working properly. I went into device manager and clicked on disk drives and my new drive doesn't show up. Do I need to worry about it not showing up?